全基因组关联研究揭示面包小麦氮、磷和钾利用效率的基因组区域

doi:10.1016/j.jia.2024.06.012

Journal of Integrative Agriculture ›› 2026, Vol. 25 ›› Issue (3): 847-863.DOI: 10.1016/j.jia.2024.06.012

全基因组关联研究揭示面包小麦氮、磷和钾利用效率的基因组区域

收稿日期:2024-02-24 修回日期:2024-06-27 接受日期:2024-05-06 出版日期:2026-03-20 发布日期:2026-02-06

Genome-wide association study reveals genomic regions for nitrogen, phosphorus and potassium use efficiency in bread wheat

Jili Xu^1*, Shuo Liu^2*, Zhiyuan Gao^1*, Qingdong Zeng³, Xiaowen Zhang¹, Dejun Han^4#, Hui Tian^1#

¹College of Natural Resources and Environment, Northwest A&F University/Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, China
²Cultivated Land Quality Protection Station, Lianyungang Agricultural and Rural Bureau, Lianyungang 712100, China
³State Key Laboratory of Crop Stress Resistance and High-Efficiency Production/College of Plant Protection, Northwest A&F University, Yangling 712100, China
⁴State Key Laboratory of Crop Stress Resistance and High-Efficiency Production/College of Agronomy, Northwest A&F University, Yangling 712100, China

Received:2024-02-24 Revised:2024-06-27 Accepted:2024-05-06 Online:2026-03-20 Published:2026-02-06
About author:Jili Xu, E-mail: 2021060380@nwafu.edu.cn; Shuo Liu, E-mail: 732361104@qq.com; Zhiyuan Gao, E-mail: 739162009@qq.com; #Correspondence Dejun Han, E-mail: handj@nwsuaf.edu.cn; Hui Tian, E-mail: tianh@nwsuaf.edu.cn
Supported by:
The work was funded by the National Key R&D Program of China (2021YFD1900700).

摘要/Abstract

摘要：

培育氮、磷、钾高效利用的小麦品种是实现农业可持续发展的重要途径。对养分利用效率的关键基因进行遗传解析和鉴定是实现这一目标的理想策略。我们利用431个不同小麦品种进行了全基因组关联分析（GWAS），揭示了1659个显著的单核苷酸多态性（SNPs）（LOD>5）。本研究在5个环境中共检测到534个与12个养分利用效率性状相关的数量性状位点（QTLs），其中14个QTLs至少在3个环境中被同时检测到。通过meta-QTL分析，发现QTL80（72.12~74.24 Mb，chr2A）、QTL387（32.88~33.56 Mb，chr6A）和QTL500（535.53-540.80 Mb，chr7B）分别与MQTL-2A-2、MQTL-6A-1和MQTL-7B-2共定位，这种趋同表明这些位点在不同环境条件下显著的相关性。在这些区域内，我们找到了与养分利用效率相关的关键候选基因，如bZIP转录因子家族基因和钾转运体基因。此外，我们还发现了一个新位点QTL234，此区域包含dof锌指蛋白、Ankyrin重复家族蛋白、细胞色素P450等关键候选基因。为了验证与氮收获指数相关的位于QTL234内的一个重要SNP，我们开发了这个位点（AX-109095537）的dCAPS标记。这些发现表明基于高分辨率SNP的GWAS在快速识别潜在关键候选基因方面的有效性，为大规模QTL精细定位、候选基因验证和功能标记的开发奠定了基础。此外，本研究鉴定出氮、磷、钾利用效率相关性状的候选基因，并开发了重要SNP的分子标记，对推进小麦养分利用效率育种进程具有重要意义。

Abstract:

The development of wheat cultivars with improved nitrogen (N), phosphorus (P), and potassium (K) use efficiency is essential for sustainable agriculture. Genetic dissection and identification of causative genes underlying nutrient use efficiency represent a key strategy toward this goal. We conducted an extensive genome-wide association study (GWAS) using a panel of 431 wheat cultivars, identifying 1,659 significant single-nucleotide polymorphisms (SNPs) (LOD>5) through genotyping-by-sequencing. This analysis revealed 534 quantitative trait loci (QTLs) associated with 12 nutrient use efficiency traits across five distinct environments, among which 14 QTLs were consistently detected in at least three environments. Notably, meta-QTL analysis, showed that QTL80 (72.12–74.24 Mb, chr2A), QTL387 (32.88–33.56 Mb, chr6A), and QTL500 (535.53–540.80 Mb, chr7B) exhibit clear co-localization with MQTL-2A-2, MQTL-6A-1, and MQTL-7B-2, respectively. This overlap highlights their robustness across diverse environmental conditions. Within these regions, critical candidate genes - including members of the bZIP transcription factor family and a potassium transporter gene - were identified in relation to nutrient use efficiency. Furthermore, a novel locus, QTL234, was discovered, harboring key candidate genes such as dof zinc finger protein, Ankyrin repeat family protein, and cytochrome P450. To validate the SNP within QTL234 associated with nitrogen harvest index (NHI), we developed a dCAPS marker for AX-109095537. These findings demonstrate the effectiveness of high-resolution SNP-based GWAS in rapidly pinpointing promising candidate genes. They also establish a foundation for large-scale QTL fine mapping, candidate gene validation, and the development of functional markers essential for enhancing nutrient use efficiency in wheat breeding programs.

Key words: wheat , genome-wide association , nutrient use efficiency , meta-QTL analysis , candidate genes

Jili Xu, Shuo Liu, Zhiyuan Gao, Qingdong Zeng, Xiaowen Zhang, Dejun Han, Hui Tian. 全基因组关联研究揭示面包小麦氮、磷和钾利用效率的基因组区域[J]. Journal of Integrative Agriculture, 2026, 25(3): 847-863.

Jili Xu, Shuo Liu, Zhiyuan Gao, Qingdong Zeng, Xiaowen Zhang, Dejun Han, Hui Tian. Genome-wide association study reveals genomic regions for nitrogen, phosphorus and potassium use efficiency in bread wheat[J]. Journal of Integrative Agriculture, 2026, 25(3): 847-863.

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全基因组关联研究揭示面包小麦氮、磷和钾利用效率的基因组区域

Genome-wide association study reveals genomic regions for nitrogen, phosphorus and potassium use efficiency in bread wheat

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